Many animals undergo migrations that depend on a range of biotic or abiotic factors provoking daily, seasonal or annual movement of individuals and/or populations. Temperate amphibians frequently have their life cycles dominated by annual temperature fluctuations, but in the tropics it is often presumed that distinct rainy seasons will influence amphibians more than small changes in temperature. Here, we direct the seasonal changes in abundance hypothesis to a caecilian amphibian Boulengerula boulengeri found in monthly randomized quantitative surveys in the top 30 cm of soil. Meteorological data are used to interpret the significant changes found in relation to rainfall and temperature variables. Instead of the expected correlation of migration with rainfall, we find that frequency varies significantly and positively with temperature. In addition, data on the depth at which individual caecilians are collected suggest that animals undergo a vertical (rather than horizontal) migration within the soil. This is the first example of vertical migrations with temperature (as opposed to rainfall) of any tropical subterranean fauna. We discuss the possible influences that stimulate migration in this species (abiotic factors, feeding, reproduction and predation). The ecology of caecilians has lagged behind that of all other tetrapods, and this study has importance for future ecological studies, as well as biodiversity assessments and monitoring methodologies.